private void collectUnknownSymbols(SymbolText st, java.util.List<String> unkwn) {
if (st != null) {
for (String s : st.getSymbols()) {
if (HGNC.getSymbol(s) == null && !unkwn.contains(s)) unkwn.add(s);
}
}
}
private static void checkZeros(ExpDataManager expMan) {
int neverabove = 0;
int sometimes = 0;
int always = 0;
Histogram h = new Histogram(0.1);
for (String gene : HGNC.getAllSymbols()) {
if (!expMan.contains(gene)) continue;
double r = expMan.getNonZeroRatio(gene);
h.count(r);
if (r == 0) neverabove++;
else if (r == 1) always++;
else sometimes++;
}
System.out.println("neverabove = " + neverabove);
System.out.println("always = " + always);
System.out.println("sometimes = " + sometimes);
h.print();
}
private void decideTargets() {
targetsToCheck = HGNC.getAllSymbols();
// targetsToCheck = getDownstream("HRAS");
}